Caister Academic Press

Software Tools for the Selection of Oligonucleotide Probes for Microarrays

Nicolas Parisot, Jérémie Denonfoux, Eric Dugat-Bony, Eric Peyretaillade and Pierre Peyret
from: Microarrays: Current Technology, Innovations and Applications (Edited by: Zhili He). Caister Academic Press, U.K. (2014)


Oligonucleotide microarrays have been widely used for gene detection and quantification of gene expression. Recently, they have been adapted for profiling microbial communities in a flexible and easy-to-use manner. In fact, it is possible to analyse both the microbial diversity and the metabolic capacity of complex communities in one experiment. However, the quality of the result is largely dependent on the quality of designed probes. Probe design, which is not a trivial task, should thus take into account multiple parameters such as the oligonucleotide sequence and its binding capacity in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative capability for each probe. Furthermore, the exploration of the not-yet-described fraction of complex communities requires consideration of the explorative power of oligonucleotide probes. To design such probes, multiple tools have been developed based on different algorithms. These algorithms and the different probe criteria that they used are described in the present chapter. However, the best algorithm to guarantee a high-quality design must be chosen with the knowledge of biological questions and biological samples read more ...
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